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tests.py
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tests.py
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import io
import ast
import json
import logging
from urllib.parse import urljoin
import uuid
import bioblend
import celery
from bioblend.galaxy.dataset_collections import (CollectionElement,
HistoryDatasetElement)
from bioblend.galaxy.histories import HistoryClient
from bioblend.galaxy.jobs import JobsClient
from bioblend.galaxy.libraries import LibraryClient
from bioblend.galaxy.workflows import WorkflowClient
from django.conf import settings
from django.contrib.auth.models import User
from django.core.management import call_command
from django.http import HttpResponseBadRequest
from django.test import TestCase, override_settings
from django_docker_engine.docker_utils import DockerClientWrapper
import mock
from guardian.shortcuts import assign_perm
from rest_framework.test import (APIRequestFactory, force_authenticate)
import constants
from analysis_manager.models import AnalysisStatus
from analysis_manager.tasks import (_galaxy_file_import,
_get_galaxy_download_task_ids,
_get_workflow_tool,
_invoke_galaxy_workflow,
_refinery_file_import,
_run_galaxy_file_import,
_run_galaxy_workflow, run_analysis)
from core.models import (INPUT_CONNECTION, OUTPUT_CONNECTION, Analysis,
AnalysisNodeConnection, AnalysisResult, ExtendedGroup,
Event, Project, WorkflowEngine)
from data_set_manager.models import Assay, Attribute, Node
from data_set_manager.utils import _create_solr_params_from_node_uuids
from factory_boy.django_model_factories import (AnnotatedNodeFactory,
AttributeFactory,
GalaxyInstanceFactory,
NodeFactory, ParameterFactory,
ToolFactory)
from factory_boy.utils import create_dataset_with_necessary_models, \
create_tool_with_necessary_models
from file_store.models import FileStoreItem
from .test_data.galaxy_mocks import (galaxy_dataset_provenance_0,
galaxy_dataset_provenance_1,
galaxy_datasets_list,
galaxy_datasets_list_same_output_names,
galaxy_history_contents,
galaxy_history_contents_same_names,
galaxy_job_a, galaxy_job_b,
galaxy_tool_data, galaxy_workflow_dict,
galaxy_workflow_dict_collection,
galaxy_workflow_invocation,
galaxy_workflow_invocation_data,
history_dataset_dict, history_dict,
library_dataset_dict, library_dict)
from tool_manager.management.commands.load_tools import \
Command as LoadToolsCommand
from .models import (GalaxyParameter, Parameter,
Tool, ToolDefinition, VisualizationTool,
VisualizationToolError, WorkflowTool)
from .utils import (create_tool,
create_tool_definition)
from .views import ToolDefinitionsViewSet, ToolsViewSet
logger = logging.getLogger(__name__)
TEST_DATA_PATH = "tool_manager/test_data"
class ToolManagerMocks(TestCase):
def setUp(self):
# Galaxy Dataset mocks
self.galaxy_datasets_list_mock = mock.patch.object(
HistoryClient, "show_matching_datasets",
return_value=galaxy_datasets_list
)
self.galaxy_datasets_list_same_names_mock = mock.patch.object(
HistoryClient, "show_matching_datasets",
return_value=galaxy_datasets_list_same_output_names
)
# Galaxy History mocks
self.history_upload_mock = mock.patch.object(
HistoryClient, "upload_dataset_from_library",
return_value=history_dataset_dict
).start()
self.delete_history_mock = mock.patch.object(
HistoryClient, "delete_history"
).start()
self.show_dataset_provenance_mock = mock.patch.object(
HistoryClient, "show_dataset_provenance"
).start()
self.show_history_mock = mock.patch.object(
HistoryClient, "show_history",
return_value=galaxy_history_contents
).start()
self.show_dataset_mock = mock.patch.object(
HistoryClient, "show_dataset",
).start()
# Galaxy Job mocks
self.show_job_mock = mock.patch.object(
JobsClient, "show_job"
).start()
# Galaxy Library mocks
self.create_library_mock = mock.patch.object(
LibraryClient,
"create_library",
return_value=library_dict
).start()
self.delete_library_mock = mock.patch.object(
LibraryClient, "delete_library"
).start()
self.library_upload_mock = mock.patch.object(
LibraryClient, "upload_file_from_url",
return_value=library_dataset_dict
).start()
# Galaxy Workflow mocks
self.delete_workflow_mock = mock.patch.object(
WorkflowClient, "delete_workflow"
).start()
self.invoke_workflow_mock = mock.patch.object(
WorkflowClient, "invoke_workflow",
return_value=galaxy_workflow_invocation_data
).start()
self.galaxy_workflow_show_invocation_mock = mock.patch.object(
WorkflowClient, "show_invocation",
return_value=galaxy_workflow_invocation
).start()
# analysis_manager mocks
self.analysis_manager_taskset_result_mock = mock.patch(
"analysis_manager.tasks.get_taskset_result",
return_value=celery.result.TaskSetResult(str(uuid.uuid4()))
).start()
# tool_manager mocks
self.get_taskset_result_mock = mock.patch(
"tool_manager.models.get_taskset_result",
return_value=celery.result.TaskSetResult(str(uuid.uuid4()))
).start()
self.create_history_mock = mock.patch.object(
WorkflowTool, "create_galaxy_history", return_value=history_dict
).start()
self.tool_data_mock = mock.patch.object(
WorkflowTool, "_get_tool_data",
return_value=galaxy_tool_data
).start()
self.get_workflow_dict_mock = mock.patch.object(
WorkflowTool, "_get_workflow_dict",
return_value=galaxy_workflow_dict
).start()
self.has_dataset_collection_input_mock_true = mock.patch.object(
WorkflowTool, "_has_dataset_collection_input", return_value=True
)
self.has_dataset_collection_input_mock_false = mock.patch.object(
WorkflowTool, "_has_dataset_collection_input", return_value=False
)
def tearDown(self):
mock.patch.stopall()
class ToolManagerTestBase(ToolManagerMocks):
# Some members in assertions are truncated if they are too long, but we
# want to see them in their entirety
maxDiff = None
FAKE_DATASET_HISTORY_ID = "0dd7fa018f646963"
GALAXY_ID_MOCK = "6fc9fbb81c497f69"
def setUp(self):
super(ToolManagerTestBase, self).setUp()
self.public_group = ExtendedGroup.objects.public_group()
self.galaxy_instance = GalaxyInstanceFactory()
self.workflow_engine = WorkflowEngine.objects.create(
instance=self.galaxy_instance
)
self.workflow_engine.set_manager_group(self.public_group.manager_group)
self.dataset = create_dataset_with_necessary_models(create_nodes=False)
self.study = self.dataset.get_latest_study()
self.assay = Assay.objects.get(study=self.study)
self.create_mock_file_relationships()
test_file = io.StringIO()
test_file.write('Coffee is really great.\n')
self.file_store_item = FileStoreItem.objects.create(
source='http://www.example.com/test_file.txt'
)
self.node = Node.objects.create(name="Node {}".format(uuid.uuid4()),
assay=self.assay, study=self.study,
file_item=self.file_store_item)
self.mock_get_workflows_reference = (
'tool_manager.management.commands.load_tools.get_workflows'
)
self.username = 'coffee_lover'
self.password = 'coffeecoffee'
self.user = User.objects.create_user(self.username, '', self.password)
self.user.save()
self.user2 = User.objects.create_user('coffee_enjoyer', '',
'coffeecoffee')
self.user2.save()
self.project = Project.objects.create(name='Catch-All Project',
is_catch_all=True)
self.project.set_owner(self.user)
self.user.profile.catch_all_project = self.project
self.user.profile.save()
self.factory = APIRequestFactory()
self.tools_view = ToolsViewSet.as_view(
{
'get': 'list',
'post': 'create',
'delete': 'destroy'
}
)
self.tool_defs_view = ToolDefinitionsViewSet.as_view(
{
'get': 'list',
'post': 'create'
}
)
self.tool_relaunch_view = ToolsViewSet.as_view({"get": "relaunch"})
self.tool_container_input_data_view = ToolsViewSet.as_view(
{"get": "container_input_data"}
)
self.tools_url_root = '/api/v2/tools/'
self.tool_defs_url_root = '/api/v2/tool_definitions/'
self.mock_parameter = ParameterFactory(
name="Test Param", description="Test Param Description",
value_type=Parameter.STRING, default_value="Coffee"
)
self.BAD_WORKFLOW_OUTPUTS = {WorkflowTool.WORKFLOW_OUTPUTS: []}
self.GOOD_WORKFLOW_OUTPUTS = {WorkflowTool.WORKFLOW_OUTPUTS: [True]}
@mock.patch("django_docker_engine.docker_utils.DockerClientWrapper.pull")
def load_visualizations(
self,
docker_pull_mock,
visualizations=["{}/visualizations/igv.json".format(TEST_DATA_PATH)]
):
call_command("load_tools", "--visualizations",
" ".join(visualizations))
return visualizations
def tearDown(self):
# Trigger the pre_delete signal so that datafiles are purged
FileStoreItem.objects.all().delete()
# Remove any running containers
DockerClientWrapper().purge_inactive(0)
super(ToolManagerTestBase, self).tearDown()
def create_solr_mock_response(self, nodes):
node_uuids = [n.uuid for n in nodes]
solr_params = _create_solr_params_from_node_uuids(node_uuids)
solr_params['json']['fields'] = solr_params['json']['filter']
solr_params['json'] = json.dumps(solr_params['json'])
return json.dumps(
{
"responseHeader": {
"status": 0,
"QTime": 36,
"params": solr_params
},
"response": {
"numFound": len(node_uuids),
"start": 0,
"docs": [
{
"uuid": node.uuid,
"name": node.name,
"type": node.type,
"file_uuid": node.file_item.uuid,
"organism_Characteristics_generic_s":
"Mus musculus",
"filename_Characteristics_generic_s":
node.file_item.source
} for node in nodes
]
}
}
)
@override_settings(CELERY_ALWAYS_EAGER=True)
def create_tool(self,
tool_type,
create_unique_name=False,
file_relationships=None,
annotation_file_name=None,
start_vis_container=False,
user_has_dataset_read_meta_access=True,
display_name=None):
if user_has_dataset_read_meta_access:
assign_perm('core.read_meta_dataset', self.user, self.dataset)
if tool_type == ToolDefinition.WORKFLOW:
self.create_workflow_tool_definition(
create_unique_name=create_unique_name,
annotation_file_name=annotation_file_name
)
launch_parameters = {
str(galaxy_param.uuid): galaxy_param.default_value
for galaxy_param in GalaxyParameter.objects.all()
}
elif tool_type == ToolDefinition.VISUALIZATION:
self.create_vis_tool_definition(
create_unique_name=create_unique_name,
annotation_file_name=annotation_file_name
)
launch_parameters = {
str(self.mock_parameter.uuid): "Edited Value"
}
else:
raise RuntimeError("Please provide a valid tool_type")
self.post_data = {
"dataset_uuid": self.dataset.uuid,
"tool_definition_uuid": self.td.uuid,
ToolDefinition.PARAMETERS: launch_parameters
}
if display_name is not None:
self.post_data["display_name"] = display_name
if file_relationships is None:
self.post_data[Tool.FILE_RELATIONSHIPS] = "[{}]".format(
self.node.uuid
)
else:
self.post_data[Tool.FILE_RELATIONSHIPS] = file_relationships
self.post_request = self.factory.post(self.tools_url_root,
data=self.post_data,
format='json')
force_authenticate(self.post_request, self.user)
# Mock the spinning up of containers
run_container_mock = mock.patch(
"django_docker_engine.docker_utils.DockerClientRunWrapper.run"
)
if tool_type == ToolDefinition.VISUALIZATION:
with mock.patch("tool_manager.models.get_solr_response_json"):
if not start_vis_container:
run_container_mock.start()
self.post_response = self.tools_view(self.post_request)
if self.post_response.status_code != 200:
return # No Tool was created
self.tool = VisualizationTool.objects.get(
tool_definition__uuid=self.td.uuid
)
# Mock the run_analysis task
elif tool_type == ToolDefinition.WORKFLOW:
with mock.patch.object(
run_analysis, 'apply_async', side_effect=None
):
self.post_response = self.tools_view(self.post_request)
assert self.post_response.status_code == 200, \
self.post_response.content
self.tool = WorkflowTool.objects.get(
tool_definition__uuid=self.td.uuid
)
self._update_galaxy_file_mapping()
self.tool.update_galaxy_data(
self.tool.GALAXY_WORKFLOW_INVOCATION_DATA,
{"id": self.GALAXY_ID_MOCK}
)
self._make_tools_get_request()
self.tool_json = self.get_response.data[0]
self.delete_request = self.factory.delete(
urljoin(self.tools_url_root, self.tool_json['uuid'])
)
force_authenticate(self.delete_request, self.user)
self.delete_response = self.tools_view(self.delete_request)
self.put_request = self.factory.put(self.tools_url_root,
data=self.tool_json,
format='json')
force_authenticate(self.put_request, self.user)
self.put_response = self.tools_view(self.put_request)
self.options_request = self.factory.options(self.tools_url_root,
data=self.tool_json,
format='json')
force_authenticate(self.options_request, self.user)
self.options_response = self.tools_view(self.options_request)
return self.tool
def create_vis_tool_definition(self, annotation_file_name=None,
create_unique_name=False):
if annotation_file_name:
self.tool_annotation = "{}/visualizations/{}".format(
TEST_DATA_PATH,
annotation_file_name
)
else:
self.tool_annotation = "{}/visualizations/igv.json".format(
TEST_DATA_PATH
)
with open(self.tool_annotation) as f:
self.tool_annotation_dict = json.loads(f.read())
if create_unique_name:
self.tool_annotation_dict["name"] = (
self.tool_annotation_dict["name"] + str(uuid.uuid4())
)
# Don't pull down images in tests
with mock.patch(
"django_docker_engine.docker_utils.DockerClientWrapper.pull",
return_value=None
) as pull_mock:
self.td = create_tool_definition(self.tool_annotation_dict)
self.assertTrue(pull_mock.called)
def create_workflow_tool_definition(self, annotation_file_name=None,
create_unique_name=False):
if annotation_file_name:
self.tool_annotation = "{}/workflows/{}".format(
TEST_DATA_PATH,
annotation_file_name
)
else:
self.tool_annotation = "{}/workflows/LIST.json".format(
TEST_DATA_PATH
)
with open(self.tool_annotation) as f:
self.tool_annotation_data = json.loads(f.read())
self.tool_annotation_data["workflow_engine_uuid"] = (
self.workflow_engine.uuid
)
if create_unique_name:
self.tool_annotation_data["name"] = (
self.tool_annotation_data["name"] + str(uuid.uuid4())
)
self.td = create_tool_definition(self.tool_annotation_data)
def create_mock_file_relationships(self):
self.LIST_BASIC = "[{}]".format(self.make_node())
self.LIST = "[{}, {}, {}, {}]".format(
*[self.make_node() for i in range(0, 4)]
)
self.LIST_LIST = "[[{}, {}], [{}, {}]]".format(
*[self.make_node() for i in range(0, 4)]
)
self.LIST_PAIR = "[({}, {}), ({}, {})]".format(
*[self.make_node() for i in range(0, 4)]
)
self.PAIR = "({}, {})".format(*[self.make_node() for i in range(0, 2)])
self.LIST_LIST_PAIR = "[[({}, {}), ({}, {})]]".format(
*[self.make_node() for i in range(0, 4)]
)
self.PAIR_LIST = "([{}, {}], [{}, {}])".format(
*[self.make_node() for i in range(0, 4)]
)
def make_node(self, source="http://www.example.com/test_file.txt"):
test_file = io.StringIO()
test_file.write('Coffee is really great.\n')
self.file_store_item = FileStoreItem.objects.create(source=source)
node = NodeFactory(name="Node {}".format(uuid.uuid4()),
assay=self.assay, study=self.study,
type=Node.RAW_DATA_FILE,
file_item=self.file_store_item)
attribute = AttributeFactory(node=node, type=Attribute.CHARACTERISTICS,
subtype='coffee', value='coffee')
AnnotatedNodeFactory(node_id=node.id, attribute_id=attribute.id,
study=self.study, assay=self.assay,
node_uuid=node.uuid,
node_file_uuid=node.file_item.uuid,
node_type=node.type, node_name=node.name,
attribute_type=attribute.type,
attribute_subtype=attribute.subtype,
attribute_value=attribute.value)
return node.uuid
def _update_galaxy_file_mapping(self):
"""
Helper method to update a WorkflowTool's
galaxy_to_refinery_mapping_list as it would be if we were
interacting with an actual Galaxy instance
"""
galaxy_to_refinery_mapping_list = []
for node in self.tool._get_input_nodes():
galaxy_to_refinery_mapping_list.append(
{
WorkflowTool.GALAXY_DATASET_HISTORY_ID:
self.FAKE_DATASET_HISTORY_ID,
Tool.REFINERY_FILE_UUID: node.file_item.uuid,
}
)
with mock.patch.object(
celery.result.TaskSetResult, 'join',
return_value=galaxy_to_refinery_mapping_list
) as join_mock:
self.tool.update_file_relationships_with_galaxy_history_data()
self.assertTrue(join_mock.called)
self.assertTrue(self.get_taskset_result_mock.called)
self.collection_description = (
self.tool._create_collection_description()
)
def test_create_valid_tool(self):
with self.assertRaises(RuntimeError):
self.create_tool("Coffee is not a valid tool type")
def _make_tools_get_request(self, user=None, tool_type=None):
request_params = {"data_set_uuid": self.dataset.uuid}
if tool_type:
request_params = dict(tool_type=tool_type, **request_params)
self.get_request = self.factory.get(
self.tools_url_root,
data=request_params
)
force_authenticate(
self.get_request,
self.user if not user else user
)
self.get_response = self.tools_view(self.get_request)
class ToolTests(ToolManagerTestBase):
def test_tool_model_str(self):
self.create_tool(ToolDefinition.VISUALIZATION)
tool = Tool.objects.get(
tool_definition__uuid=self.td.uuid
)
self.assertEqual(
tool.__str__(),
"Tool: Test LIST Visualization IGV"
)
def test_tool_container_removed_on_deletion(self):
self.create_tool(ToolDefinition.VISUALIZATION)
with mock.patch(
"django_docker_engine.docker_utils.DockerClientWrapper"
".purge_by_label"
) as purge_mock:
Tool.objects.get(tool_definition__uuid=self.td.uuid).delete()
self.assertTrue(purge_mock.called)
def test_node_uuids_get_populated_with_urls(self):
vis_tool = self.create_tool(
ToolDefinition.VISUALIZATION,
file_relationships=self.LIST
)
file_relationships = vis_tool.get_file_relationships_urls()
for url in file_relationships:
self.assertIn("test_file.txt", url)
def test_get_file_relationships_urls(self):
self.create_tool(ToolDefinition.WORKFLOW)
self.assertEqual(
self.tool.get_file_relationships_urls(),
['http://www.example.com/test_file.txt']
)
def test_update_galaxy_data(self):
self.create_tool(ToolDefinition.WORKFLOW)
self.tool.update_galaxy_data("test", "data")
self.tool.update_galaxy_data("more", "data")
self.assertEqual(
self.tool.get_galaxy_dict(),
{
WorkflowTool.FILE_RELATIONSHIPS_GALAXY: (
str(
self.tool.get_galaxy_file_relationships()
).replace("'", '"')
),
WorkflowTool.GALAXY_TO_REFINERY_MAPPING_LIST: [
{
self.tool.GALAXY_DATASET_HISTORY_ID:
self.FAKE_DATASET_HISTORY_ID,
self.tool.REFINERY_FILE_UUID: self.node.file_item.uuid,
WorkflowTool.ANALYSIS_GROUP: 0
}
],
WorkflowTool.GALAXY_WORKFLOW_INVOCATION_DATA: {
"id": self.GALAXY_ID_MOCK
},
"test": "data",
"more": "data"
}
)
def test_creating_vis_tool_doesnt_set_tool_launch_config_galaxy_data(self):
self.create_tool(ToolDefinition.VISUALIZATION)
with self.assertRaises(KeyError):
self.tool.get_tool_launch_config()[WorkflowTool.GALAXY_DATA]
def test_set_analysis_bad_uuid(self):
self.create_tool(ToolDefinition.WORKFLOW)
with self.assertRaises(RuntimeError):
self.tool.set_analysis(str(uuid.uuid4()))
def test_tool_launch_method_raises_error_when_not_overridden(self):
self.create_workflow_tool_definition()
tool = ToolFactory(
dataset=self.dataset,
tool_definition=self.td
)
with self.assertRaises(NotImplementedError) as context:
tool.launch()
self.assertEqual(str(context.exception), tool.LAUNCH_WARNING)
def test__get_owner_info_as_dict(self):
self.create_tool(ToolDefinition.VISUALIZATION)
self._make_tools_get_request()
self.assertEqual(
self.get_response.data[0]["owner"],
{
"username": self.user.username,
"full_name": "{} {}".format(self.user.first_name,
self.user.last_name),
"user_profile_uuid": str(self.user.profile.uuid)
}
)
def test_relaunch_url(self):
self.create_tool(ToolDefinition.VISUALIZATION)
self.assertEqual(self.tool.relaunch_url,
"/api/v2/tools/{}/relaunch/".format(self.tool.uuid))
def test_get_relative_container_url(self):
self.create_tool(ToolDefinition.VISUALIZATION)
self.assertEqual(
self.tool.get_relative_container_url(),
"/{}/{}".format(settings.DJANGO_DOCKER_ENGINE_BASE_URL,
self.tool.container_name)
)
def test_is_workflow(self):
self.create_tool(ToolDefinition.WORKFLOW)
self.assertTrue(self.tool.is_workflow())
self.assertFalse(self.tool.is_visualization())
def test_is_visualization(self):
self.create_tool(ToolDefinition.VISUALIZATION)
self.assertTrue(self.tool.is_visualization())
self.assertFalse(self.tool.is_workflow())
def test_visualization_is_running(self):
self.create_tool(
ToolDefinition.VISUALIZATION,
start_vis_container=True
)
self.assertTrue(self.tool.is_running())
DockerClientWrapper().purge_inactive(0)
self.assertFalse(self.tool.is_running())
def test_workflow_is_running(self):
self.create_tool(ToolDefinition.WORKFLOW)
self.tool.analysis.set_status(Analysis.RUNNING_STATUS)
self.assertTrue(self.tool.is_running())
self.tool.analysis.set_status(Analysis.SUCCESS_STATUS)
self.assertFalse(self.tool.is_running())
def test_terminate_file_import_tasks(self):
with mock.patch(
"file_store.models.FileStoreItem.terminate_file_import_task"
) as terminate_mock:
self.create_tool(ToolDefinition.WORKFLOW)
self.tool.analysis.terminate_file_import_tasks()
self.assertEqual(terminate_mock.call_count, 1)
def test_tool_launch_has_reasonable_default_display_name(self):
self.create_tool(tool_type=ToolDefinition.VISUALIZATION)
self.assertEqual(
self.tool.display_name,
" ".join([self.tool.name, self.tool.formatted_creation_date,
self.user.username])
)
class VisualizationToolTests(ToolManagerTestBase):
def setUp(self):
super(VisualizationToolTests, self).setUp()
self.visualization_tool = self.create_tool(
ToolDefinition.VISUALIZATION,
file_relationships=self.LIST
)
self.search_solr_mock = mock.patch(
"data_set_manager.utils.search_solr",
return_value=self.create_solr_mock_response(
self.visualization_tool._get_input_nodes()
)
).start()
def _create_detailed_nodes_dict(self, nodes):
return {
node.uuid: {
'file_url': self.node.file_item.get_datafile_url(),
'auxiliary_file_list': self.node.get_auxiliary_node_uuids(),
VisualizationTool.NODE_SOLR_INFO: {
'uuid': node.uuid,
'name': node.name,
'type': node.type,
'file_uuid': node.file_item.uuid,
'organism_Characteristics_generic_s': 'Mus musculus',
'filename_Characteristics_generic_s': node.file_item.source
}
} for node in nodes
}
def test_get_detailed_input_nodes_dict(self):
input_nodes_meta_info = self.tool._get_detailed_nodes_dict(
self.tool.get_input_node_uuids()
)
self.assertEqual(
input_nodes_meta_info,
self._create_detailed_nodes_dict(self.tool._get_input_nodes())
)
self.assertTrue(self.search_solr_mock.called)
def test_get_detailed_input_nodes_dict_all_dataset_nodes(self):
self.search_solr_mock.return_value = self.create_solr_mock_response(
self.tool.dataset.get_nodes()
)
all_dataset_nodes_meta_info = self.tool._get_detailed_nodes_dict(
self.tool.dataset.get_node_uuids()
)
self.assertEqual(
all_dataset_nodes_meta_info,
self._create_detailed_nodes_dict(self.tool.dataset.get_nodes())
)
self.assertTrue(self.search_solr_mock.called)
def test_get_container_input_dict(self):
tool_input_dict = self.tool.get_container_input_dict()
file_relationships = self.tool.get_file_relationships_urls()
self.assertEqual(
tool_input_dict,
{
VisualizationTool.API_PREFIX:
self.tool.get_relative_container_url() + "/",
Tool.FILE_RELATIONSHIPS: file_relationships,
VisualizationTool.INPUT_NODE_INFORMATION:
self.tool._get_detailed_nodes_dict(
self.tool.get_input_node_uuids()
),
VisualizationTool.ALL_NODE_INFORMATION:
self.tool._get_detailed_nodes_dict(
self.tool.dataset.get_node_uuids()
),
ToolDefinition.PARAMETERS:
self.tool._get_visualization_parameters(),
ToolDefinition.EXTRA_DIRECTORIES:
self.tool.tool_definition.get_extra_directories()
}
)
self.assertTrue(self.search_solr_mock.called)
def test__get_visualization_parameters(self):
parameter = self.visualization_tool.tool_definition.get_parameters()[0]
self.assertEqual(
self.visualization_tool._get_visualization_parameters(),
[
{
"description": parameter.description,
"default_value": parameter.default_value,
"uuid": str(parameter.uuid),
"name": parameter.name,
"value": parameter.default_value,
"value_type": parameter.value_type
}
]
)
def test__get_edited_parameter_value(self):
edited_parameter_value = (
self.visualization_tool._get_edited_parameter_value(
self.mock_parameter
)
)
self.assertEqual(edited_parameter_value, "Edited Value")
parameter = ParameterFactory(
name="Test Param",
description="Test Param Description",
value_type=Parameter.STRING,
default_value="Coffee"
)
non_edited_parameter_value = (
self.visualization_tool._get_edited_parameter_value(parameter)
)
self.assertEqual(non_edited_parameter_value, parameter.default_value)
class WorkflowToolTests(ToolManagerTestBase):
def setUp(self):
super(WorkflowToolTests, self).setUp()
self.show_dataset_provenance_side_effect = [
galaxy_dataset_provenance_0, galaxy_dataset_provenance_0,
galaxy_dataset_provenance_1, galaxy_dataset_provenance_1
]
self.show_job_side_effect = [galaxy_job_a, galaxy_job_a,
galaxy_job_b, galaxy_job_b]
def _assert_analysis_node_connection_outputs_validity(self):
input_connection = AnalysisNodeConnection.objects.filter(
analysis=self.tool.analysis,
direction=INPUT_CONNECTION
)[0]
assay = input_connection.node.assay
study = input_connection.node.study
output_connections = AnalysisNodeConnection.objects.filter(
analysis=self.tool.analysis,
direction=OUTPUT_CONNECTION
)
self.assertGreater(output_connections.count(), 0)
for output_connection in output_connections:
self.assertEqual(output_connection.node.study, study)
self.assertEqual(output_connection.node.assay, assay)
self.assertEqual(output_connection.node.name,
output_connection.name)
self.assertEqual(output_connection.node.analysis_uuid,
self.tool.analysis.uuid)
self.assertEqual(output_connection.node.subanalysis,
output_connection.subanalysis)
self.assertEqual(output_connection.node.workflow_output,
output_connection.name)
def test_list_dataset_collection_description_creation(self):
self.create_tool(
ToolDefinition.WORKFLOW,
file_relationships=self.LIST_BASIC
)
self.assertEqual(
self.collection_description.type,
WorkflowTool.LIST
)
self.assertEqual(
len(self.collection_description.elements),
1
)
for element in self.collection_description.elements:
self.assertEqual(
type(element),
HistoryDatasetElement
)
def test_list_pair_dataset_collection_description_creation(self):
self.create_tool(
ToolDefinition.WORKFLOW,
file_relationships=self.LIST_PAIR
)
self.assertEqual(
self.collection_description.type,
"{}:{}".format(WorkflowTool.LIST, WorkflowTool.PAIRED)
)
self.assertEqual(
len(self.collection_description.elements),
2
)
for element in self.collection_description.elements:
self.assertEqual(type(element), CollectionElement)
self.assertEqual(element.type, WorkflowTool.PAIRED)
self.assertEqual(len(element.elements), 2)
for el in element.elements:
self.assertEqual(type(el), HistoryDatasetElement)
self.assertEqual(
element.elements[0].to_dict()["name"],
WorkflowTool.FORWARD
)
self.assertEqual(
element.elements[1].to_dict()["name"],
WorkflowTool.REVERSE
)
def test_paired_dataset_collection_creation(self):
self.create_tool(
ToolDefinition.WORKFLOW,
file_relationships=self.PAIR
)
self.assertEqual(
self.collection_description.type,
WorkflowTool.PAIRED
)
self.assertEqual(len(self.collection_description.elements), 2)
for element in self.collection_description.elements:
self.assertEqual(type(element), HistoryDatasetElement)
self.assertEqual(
self.collection_description.elements[0].to_dict()["name"],
WorkflowTool.FORWARD
)
self.assertEqual(
self.collection_description.elements[1].to_dict()["name"],
WorkflowTool.REVERSE
)
def test_paired_list_dataset_collection_description_creation(self):
self.create_tool(
ToolDefinition.WORKFLOW,
file_relationships=self.PAIR_LIST
)
self.assertEqual(
self.collection_description.type,
"{}:{}".format(WorkflowTool.PAIRED, WorkflowTool.LIST)
)
self.assertEqual(len(self.collection_description.elements), 2)
for element in self.collection_description.elements:
self.assertEqual(type(element), CollectionElement)
self.assertEqual(element.type, WorkflowTool.LIST)
for el in element.elements:
self.assertEqual(type(el), HistoryDatasetElement)
def test_list_list_paired_dataset_collection_creation(self):
self.create_tool(
ToolDefinition.WORKFLOW,
file_relationships=self.LIST_LIST_PAIR
)
self.assertEqual(
self.collection_description.type,
"{}:{}:{}".format(
WorkflowTool.LIST,
WorkflowTool.LIST,
WorkflowTool.PAIRED
)
)
self.assertEqual(len(self.collection_description.elements), 1)
for element in self.collection_description.elements:
self.assertEqual(type(element), CollectionElement)
self.assertEqual(element.type, WorkflowTool.LIST)
self.assertEqual(len(element.elements), 2)
for el in element.elements:
self.assertEqual(el.type, WorkflowTool.PAIRED)
self.assertEqual(len(element.elements), 2)
for thing in el.elements:
self.assertEqual(type(thing), HistoryDatasetElement)
self.assertEqual(
el.elements[0].to_dict()["name"],
WorkflowTool.FORWARD
)
self.assertEqual(
el.elements[1].to_dict()["name"],
WorkflowTool.REVERSE
)
def test_galaxy_collection_type_pair(self):
self.create_tool(
ToolDefinition.WORKFLOW,
file_relationships=self.PAIR
)
self.assertEqual(
self.tool.galaxy_collection_type,
WorkflowTool.PAIRED
)
def test_galaxy_collection_type_list_pair(self):
self.create_tool(
ToolDefinition.WORKFLOW,
file_relationships=self.LIST_PAIR
)
self.assertEqual(
self.tool.galaxy_collection_type,
"{}:{}".format(
WorkflowTool.LIST,
WorkflowTool.PAIRED
)
)
def test_galaxy_collection_type_pair_list(self):